EnhancerDB: a resource of transcriptional regulation in the context of enhancers | Zendy

Ran Kang | Zendy; Yiming Zhang | Zendy; Qingqing Huang | Zendy; Junhua Meng | Zendy; Ruofan Ding | Zendy; Yunjian Chang | Zendy; Lili Xiong | Zendy; Zhiyun Guo | Zendy

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EnhancerDB: a resource of transcriptional regulation in the context of enhancers

Author(s) -

Ran Kang,

Yiming Zhang,

Qingqing Huang,

Junhua Meng,

Ruofan Ding,

Yunjian Chang,

Lili Xiong,

Zhiyun Guo

Publication year - 2018

Publication title -

database

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 1.406

H-Index - 62

ISSN - 1758-0463

DOI - 10.1093/database/bay141

Subject(s) - enhancer , biology , gene , microrna , context (archaeology) , computational biology , regulatory sequence , regulation of gene expression , enhancer rnas , expression quantitative trait loci , genetics , transcription factor , single nucleotide polymorphism , paleontology , genotype

Enhancers can act as cis-regulatory elements to control transcriptional regulation by recruiting DNA-binding transcription factors (TFs) in a tissue-specific manner. Recent studies show that enhancers regulate not only protein-coding genes but also microRNAs (miRNAs), and mutations within the TF binding sites (TFBSs) located on enhancers will cause a variety of diseases such as cancer. However, a comprehensive resource to integrate these regulation elements for revealing transcriptional regulations in the context of enhancers is not currently available. Here, we introduce EnhancerDB, a web-accessible database to provide a resource to browse and search regulatory relationships identified in this study, including 131 054 581 TF-enhancer, 17 059 enhancer-miRNAs, 318 993 enhancer-genes, 4 639 558 TF-miRNAs, 1 059 695 TF-genes, 11 439 394 enhancer-single-nucleotide polymorphisms (SNPs) and 23 334 genes associated with expression quantitative trait loci (eQTL) SNP and expression profile of TF/gene/miRNA across multiple human tissues/cell lines. We also developed a tool that further allows users to define tissue-specific enhancers by setting the threshold score of tissue specificity of enhancers. In addition, links to external resources are also available at EnhancerDB.

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